Web Resources for Mass Spectrometry-based Proteomics

With the development of high-resolution and high-throughput mass spectrometry(MS)technology, a large quantum of proteomic data is continually being generated. Collecting and sharing these data are a challenge that requires immense and sustained human effort. In this report, we provide a classification of important web resources for MS-based proteomics and present rating of these web resources, based on whether raw data are stored, whether data submission is supported,and whether data analysis pipelines are provided. These web resources are important for biologists involved in proteomics research.     

蛋白质质谱分析的无标记定量算法研究进展

作为发现疾病相关生物标志物的重要途径,定量研究已成为蛋白质组学的热点问题.随着实验方法的发展和改进,定量数据处理算法也在不断更新和完善.将现有的无标记定量方法归纳为需要/不需要鉴定结果两类方法,分析比较了两类方法的异同及优缺点,详细讨论了所涉及的主要算法,总结了一些常用的无标记定量软件及对应的网络资源.展望了无标记定量数据分析的未来研究方向.     

YPED:An Integrated Bioinformatics Suite and Database for Mass Spectrometry-based Proteomics Research

We report a significantly-enhanced bioinformatics suite and database for proteomics research called Yale Protein Expression Database(YPED) that is used by investigators at more than 300 institutions worldwide. YPED meets the data management, archival, and analysis needs of a high-throughput mass spectrometry-based proteomics research ranging from a singlelaboratory, group of laboratories within and beyond an institution, to the entire proteomics community. The current version is a significant improvement over the first version in that it contains new modules for liquid chromatography–tandem mass spectrometry(LC–MS/MS) database search results, label and label-free quantitative proteomic analysis, and several scoring outputs for phosphopeptide site localization. In addition, we have added both peptide and protein comparative analysis tools to enable pairwise analysis of distinct peptides/proteins in each sample and of overlapping peptides/proteins between all samples in multiple datasets. We have also implemented a targeted proteomics module for automated multiple reaction monitoring(MRM)/selective reaction monitoring(SRM) assay development. We have linked YPED's database search results and both label-based and label-free fold-change analysis to the Skyline Panorama repository for online spectra visualization. In addition, we have built enhanced functionality to curate peptide identifications into an MS/MS peptide spectral library for all of our protein database search identification results.     

Enhanced Sensitivity for Selected Reaction Monitoring Mass Spectrometry-based Targeted Proteomics Using a Dual Stage Electrodynamic Ion Funnel Interface

Selected reaction monitoring mass spectrometry (SRM-MS) is playing an increasing role in quantitative proteomics and biomarker discovery studies as a method for high throughput candidate quantification and verification. Although SRM-MS offers advantages in sensitivity and quantification compared with other MS-based techniques, current SRM technologies are still challenged by detection and quantification of low abundance proteins (e.g. present at ∼10 ng/ml or lower levels in blood plasma). Here we report enhanced detection sensitivity and reproducibility for SRM-based targeted proteomics by coupling a nanospray ionization multicapillary inlet/dual electrodynamic ion funnel interface to a commercial triple quadrupole mass spectrometer. Because of the increased efficiency in ion transmission, significant enhancements in overall signal intensities and improved limits of detection were observed with the new interface compared with the original interface for SRM measurements of tryptic peptides from proteins spiked into non-depleted mouse plasma over a range of concentrations. Overall, average SRM peak intensities were increased by ∼70-fold. The average level of detection for peptides also improved by ∼10-fold with notably improved reproducibility of peptide measurements as indicated by the reduced coefficients of variance. The ability to detect proteins ranging from 40 to 80 ng/ml within mouse plasma was demonstrated for all spiked proteins without the application of front-end immunoaffinity depletion and fractionation. This significant improvement in detection sensitivity for low abundance proteins in complex matrices is expected to enhance a broad range of SRM-MS applications including targeted protein and metabolite validation.Although mass spectrometry (MS)-based proteomics is a promising high throughput technology for biomarker discovery and validation (1–5), only a handful of cancer biomarkers have been approved by the United States Food and Drug Administration for clinical use in the last decade (6, 7). Assuming that low abundance biomarkers do exist in the biofluids to be studied, the success of biomarker discovery efforts primarily depends on the sensitivity, accuracy, and robustness of the measurement technologies; the quality and size of patient cohorts and clinical samples and execution within the context of an overall difficult and expensive path to clinical application that encompasses discovery, verification, and validation stages (1, 5, 8–10). A multiplexed assay platform increasingly considered for biomarker verification is selected reaction monitoring (SRM)¹ by tandem mass spectrometry using e.g. a triple quadrupole (QqQ) mass spectrometer to attain high throughput quantitative measurements of targeted proteins in complex matrices (1, 11, 12).SRM utilizes two stages of mass filtering by selecting a specific analyte ion of interest (precursor ion) in the first stage followed by a specific fragment ion derived from the precursor (fragment ion) filter in the second stage after collision-activated dissociation. Typically, several transitions (precursor/fragment ion pairs) are monitored for greater selectivity and confidence in a targeted peptide assay, and large numbers of peptides can be monitored during a single LC-MS/MS analysis. The two-stage mass selection by individual quadrupoles enables more rapid and continuous monitoring of specific ions derived from analytes of interest such as peptides and leads to significantly enhanced detection sensitivity and quantitative accuracy compared with broad (i.e. non-targeted) LC-MS or LC-MS/MS measurements (11, 12). Both the sensitivity and selectivity of SRM-MS make this technique well suited for the targeted detection and quantification of low abundance proteins in highly complex biofluids (13–16). The precision and reproducibility of SRM-based measurements of proteins in plasma across different laboratories have recently been assessed (17).Despite its promise, present SRM measurements still do not provide sufficient sensitivity for reliable detection and quantification of low abundance proteins in biofluids (e.g. present in plasma at ∼10 ng/ml or lower levels) primarily because of factors related to high sample complexity and the large dynamic range of relative protein abundances (7, 18, 19). Given sufficient selectivity, the sensitivity achievable is generally related to the peptide MS and MS/MS signal intensities obtained. One of the key factors limiting peptide MS intensities is the significant ion losses encountered between the electrospray ionization (ESI) source and the interface to the mass spectrometer. In typical LC-ESI-MS interfaces, the mass spectrometer inlet (e.g. heated capillary followed by a skimmer) presently provides total ion utilization and ion transmission efficiencies on the order of ∼1% (20) due to a combination of limited ion sampling from the atmospheric pressure ion source into the inlet and inefficient transmission of ions entering the first reduced pressure stage of the mass spectrometer.The electrodynamic ion funnel (21), which has been developed to efficiently capture, focus, and transmit ions to the high vacuum region of the mass spectrometer, is expected to provide a large benefit to SRM analyses. The original ion funnel interfaces, which operated at a maximum of ∼5 torr, were able to enhance signal intensities for a variety of MS analyzers (22–24) by replacing the inefficient skimmer interface. Although achieving near lossless ion transmission to high vacuum, losses at the atmospheric pressure interface went unmitigated. More recently, a high pressure ion funnel interface capable of operating at a pressure of ∼30 torr was introduced (25). The higher operating pressures accommodated greater gas loads and enabled more efficient ion sampling from atmospheric pressure through a multicapillary inlet. With a dual ion funnel interface comprising a high pressure ion funnel with a heated multicapillary inlet followed by a standard ion funnel operated at 1–2 torrs, highly efficient ion sampling from atmospheric pressure to high vacuum is readily achieved.In this study, we report the enhanced sensitivity and reproducibility of SRM-based targeted proteomics measurements achieved by implementing a dual stage electrodynamic ion funnel interface that incorporates a multicapillary inlet with a triple quadrupole mass spectrometer. A series of LC-SRM-MS measurements were made using mouse plasma samples spiked with various concentrations of tryptic peptides from five standard proteins to evaluate the improvements in detection sensitivity and reproducibility attained by this modified interface relative to a standard Thermo (single capillary inlet/skimmer) interface. A ∼10-fold improvement in the limit of detection (LOD) as well as improved measurement reproducibility was achieved.     

Mass Spectrometry-based Quantitative Proteomic Profiling of Human Pancreatic and Hepatic Stellate Cell Lines

The functions of the liver and the pancreas differ; however, chronic inflammation in both organs is associated with fibrosis. Evidence suggests that fibrosis in both organs is partially regulated by organ-specific stellate cells. We explore the proteome of human hepatic stellate cells (hHSC) and human pancreatic stellate cells (hPaSC) using mass spectrometry (MS)-based quantitative proteomics to investigate pathophysiologic mechanisms. Proteins were isolated from whole cell lysates of immortalized hHSC and hPaSC. These proteins were tryptically digested, labeled with tandem mass tags (TMT), fractionated by OFFGEL, and subjected to MS. Proteins significantly different in abundance (P < 0.05) were classified via gene ontology (GO) analysis. We identified 1223 proteins and among them, 1222 proteins were quantifiable. Statistical analysis determined that 177 proteins were of higher abundance in hHSC, while 157 were of higher abundance in hPaSC. GO classification revealed that proteins of relatively higher abundance in hHSC were associated with protein production, while those of relatively higher abundance in hPaSC were involved in cell structure. Future studies using the methodologies established herein, but with further upstream fractionation and/or use of enhanced MS instrumentation will allow greater proteome coverage, achieving a comprehensive proteomic analysis of hHSC and hPaSC.     

Comprehensive Profiling of Cartilage Extracellular Matrix Formation and Maturation Using Sequential Extraction and Label-free Quantitative Proteomics

Articular cartilage is indispensable for joint function but has limited capacity for self-repair. Engineering of neocartilage in vitro is therefore a major target for autologous cartilage repair in arthritis. Previous analysis of neocartilage has targeted cellular organization and specific molecular components. However, the complexity of extracellular matrix (ECM) development in neocartilage has not been investigated by proteomics. To redress this, we developed a mouse neocartilage culture system that produces a cartilaginous ECM. Differential analysis of the tissue proteome of 3-week neocartilage and 3-day postnatal mouse cartilage using solubility-based protein fractionation targeted components involved in neocartilage development, including ECM maturation. Initially, SDS-PAGE analysis of sequential extracts revealed the transition in protein solubility from a high proportion of readily soluble (NaCl-extracted) proteins in juvenile cartilage to a high proportion of poorly soluble (guanidine hydrochloride-extracted) proteins in neocartilage. Label-free quantitative mass spectrometry (LTQ-Orbitrap) and statistical analysis were then used to filter three significant protein groups: proteins enriched according to extraction condition, proteins differentially abundant between juvenile cartilage and neocartilage, and proteins with differential solubility properties between the two tissue types. Classification of proteins differentially abundant between NaCl and guanidine hydrochloride extracts (n = 403) using bioinformatics revealed effective partitioning of readily soluble components from subunits of larger protein complexes. Proteins significantly enriched in neocartilage (n = 78) included proteins previously not reported or with unknown function in cartilage (integrin-binding protein DEL1; coiled-coil domain-containing protein 80; emilin-1 and pigment epithelium derived factor). Proteins with differential extractability between juvenile cartilage and neocartilage included ECM components (nidogen-2, perlecan, collagen VI, matrilin-3, tenascin and thrombospondin-1), and the relationship between protein extractability and ECM ultrastructural organization was supported by electron microscopy. Additionally, one guanidine extract-specific neocartilage protein, protease nexin-1, was confirmed by immunohistochemistry as a novel component of developing articular cartilage in vivo. The extraction profile and matrix-associated immunostaining implicates protease nexin-1 in cartilage development in vitro and in vivo.The cartilage of the mammalian skeletal system has two distinct roles. The epiphyseal cartilage of the growth plate drives endochondral bone growth, and the hyaline cartilage at the weight-bearing surfaces of bones facilitates joint articulation. In both environments, chondrocyte-regulated production, assembly, and turnover of the extracellular matrix (ECM)¹ are essential for the tissue to withstand compressive forces and respond to mechanical loading. The major structural constituents of cartilage ECM are the heterotypic collagen II/IX/XI fibrils and proteoglycan-glycosaminoglycan networks of aggrecan and hyaluronan. Loss of joint function in osteoarthritis (OA) is strongly associated with net loss of aggrecan and collagen breakdown caused by an imbalance of ECM homeostasis (1). In addition, many inherited human chondrodysplasias involve disruption of cartilage matrix assembly or cell-matrix interactions, resulting in abnormal skeletal development and in some cases early onset cartilage degeneration (2, 3).The alterations in chondrocyte metabolism that occur during OA are complex and remain poorly understood (4). An early response to loss or fragmentation of ECM components is attempted tissue repair through secretion of anabolic factors, cell proliferation, and matrix remodeling (5). However, the resulting product is a fibrocartilage that does not recapitulate the composition or precise architecture of the original hyaline articular cartilage. This limited capacity of cartilage for regeneration has driven research into cartilage tissue engineering (6). Production of authentic hyaline cartilage in vitro remains challenging due to the dedifferentiation of primary chondrocytes upon removal from their three-dimensional matrix environment (7). However, improved “neocartilage” culture systems have been developed through evaluation of suitable chondroprogenitor or chondrocyte subpopulations and optimization of exogenous support matrices and growth factors (8, 9). The therapeutic target of neocartilage culture is autologous tissue repair. However, there is fundamental value in using neocartilage systems to elucidate mechanisms of protein integration into the ECM and the role of specific protein interactions during cartilage maturation.Cartilage profiling by 2-DE and mass spectrometry-based proteomics is generating important new insight into mechanisms of cartilage degeneration in vitro and in vivo (10). For example, anabolic factors with potential roles in cartilage repair, including connective tissue growth factor and inhibin βA (activin), were identified in the secretome of human OA cartilage explants (11). Comparison of cartilage protein extracts from normal donors and OA patients revealed significantly increased levels of the serine protease Htra1 in patient cartilage (12) and that Htra1-mediated proteolysis of aggrecan may significantly contribute to OA pathology (13). Targeted analysis of the chondrocyte mitochondrial proteome highlighted OA-related changes in energy production and protection against reactive oxygen species (14). Obtaining sufficient chondrocytes from human donors for proteomics unfortunately requires expansion of the cell population with potential loss of the chondrocyte phenotype during prolonged culture. Other drawbacks encountered with human samples include the clinical heterogeneity of OA, lack of matched controls, and inherent genetic variation of human subjects (15). Alternatively, animal models that recapitulate hallmarks of progressive cartilage degeneration, such as aggrecan loss and articular surface fibrillation, are emerging as a powerful resource, particularly in mice lacking specific proteases or protease target sites (16, 17). The development of techniques for analysis of murine cartilage using proteomics has paved the way for differential analysis of normal and pathological or genetically targeted cartilage (18, 19).Label-free methods for relative peptide quantitation, such as ion intensity measurement and spectral counting, are emerging as reliable and cost-effective alternatives to chemical modification or isotopic peptide labeling (20). Combining orthogonal protein and/or peptide fractionation with high resolution HPLC-MS can achieve proteome-wide coverage (21). Because extensive sample fractionation can introduce redundancy and variation, improved sequence/proteome coverage must be balanced against the cost of additional sample handling and lengthy LC-MS runs (22).Here we describe a novel platform for analysis of mouse cartilage using solubility-based protein fractionation (19) combined with label-free quantitative tandem MS (LTQ-Orbitrap). Sequential extraction of 3-day postnatal (P3) mouse epiphyseal cartilage and 3-week neocartilage cultures revealed a marked transition from a high proportion of readily soluble components in P3 extracts to a greater proportion of poorly soluble proteins in neocartilage. Principal component analysis and hierarchical clustering were used to globally assess the inter-relationships between P3 cartilage and neocartilage NaCl and guanidine hydrochloride (GdnHCl) extracts. At a p value cutoff of 0.05, 403 proteins were classified as extract-specific, whereas 125 proteins were classified as tissue sample-specific. Many of the proteins significantly enriched in neocartilage were annotated by the terms cell adhesion, extracellular matrix, and cytoskeletal remodeling. Further statistical analysis identified a third important protein category in which protein solubility was altered between the P3 and neocartilage. Identification of proteins involved in neocartilage maturation has generated novel insight into the fundamental process of cartilage matrix development with potential for further analysis of engineered cartilaginous tissues with biomedical applications.     

A Targeted Quantitative Proteomics Strategy for Global Kinome Profiling of Cancer Cells and Tissues

Kinases are among the most intensively pursued enzyme superfamilies as targets for anti-cancer drugs. Large data sets on inhibitor potency and selectivity for more than 400 human kinases became available recently, offering the opportunity to design rationally novel kinase-based anti-cancer therapies. However, the expression levels and activities of kinases are highly heterogeneous among different types of cancer and even among different stages of the same cancer. The lack of effective strategy for profiling the global kinome hampers the development of kinase-targeted cancer chemotherapy. Here, we introduced a novel global kinome profiling method, based on our recently developed isotope-coded ATP-affinity probe and a targeted proteomic method using multiple-reaction monitoring (MRM), for assessing simultaneously the expression of more than 300 kinases in human cells and tissues. This MRM-based assay displayed much better sensitivity, reproducibility, and accuracy than the discovery-based shotgun proteomic method. Approximately 250 kinases could be routinely detected in the lysate of a single cell line. Additionally, the incorporation of iRT into MRM kinome library rendered our MRM kinome assay easily transferrable across different instrument platforms and laboratories. We further employed this approach for profiling kinase expression in two melanoma cell lines, which revealed substantial kinome reprogramming during cancer progression and demonstrated an excellent correlation between the anti-proliferative effects of kinase inhibitors and the expression levels of their target kinases. Therefore, this facile and accurate kinome profiling assay, together with the kinome-inhibitor interaction map, could provide invaluable knowledge to predict the effectiveness of kinase inhibitor drugs and offer the opportunity for individualized cancer chemotherapy.Protein phosphorylation, one of the most important types of post-translational modifications (PTMs)¹, is catalyzed by protein kinases (collectively referred to as the kinome), which are encoded by over 500 genes in higher eukaryotes (1). Aberrant expression and/or activation/deactivation of kinases have been implicated as among the major mechanisms through which cancer cells escape normal physiological constraints of cell growth and survival (2). Additionally, dynamic kinome reprogramming has been found to be closely associated with resistance toward cancer chemotherapy (3). Owing to their crucial roles in cancer development, kinases have become one of the most intensively pursued enzyme superfamilies as drug targets for cancer chemotherapy and more than 130 distinct kinase inhibitors have been developed for phase 1–3 clinical trials (4). Recently, inhibitor potency and selectivity for more than 400 kinases have been reported, which provided a comprehensive target-inhibition profile for the majority of the human kinome (5–7). Therefore, the kinome-inhibitor interaction networks coupled with comprehensive profiling of global kinome expression and activity associated with certain types of cancer could be invaluable for understanding the mechanisms of carcinogenesis and for designing rationally novel kinase-directed anti-cancer chemotherapies.Unfortunately, currently there is no optimal strategy for profiling the expression levels of the entire kinome at the protein level. Traditional methods for measuring kinase expression rely primarily on antibody-based immunoassays because of their high specificity and sensitivity (8). The immunoassays, however, are limited by the availability of high-quality antibodies; therefore, these methods are only useful for assessing a small number of kinases in low-throughput. Recent advances in MS instrumentation and bioinformatic tools enable the identification and quantification of a significant portion of the human proteome from complex samples (9). However, proteomic studies of global kinome by MS are still very challenging, which is largely attributed to the fact that, similar as other regulatory enzymes, protein kinases are generally expressed at low levels in cells (10). This analytical challenge is further aggravated in shotgun proteomics approach where even more complex mixtures of peptides instead of proteins from whole cell or tissue extracts are analyzed (11). Therefore, selective enrichment of protein kinases from cellular extracts is essential for the comprehensive identification and quantification of the global kinome.Affinity columns immobilized with kinase inhibitors have been employed as capture ligands for the enrichment of kinases, and ∼200 protein kinases could be identified and quantified by subsequent LC-MS/MS analyses (3, 10, 12). Recently, we and others reported the application of biotin-conjugated acyl nucleotide probes for the enrichment and identification of kinases from complex protein mixtures (13–17). This enrichment technique, in combination with multi-dimensional LC-MS platform, facilitates the identification of ∼200 protein kinases (15). Despite these advances, such large-scale kinome studies are often performed in the data-dependent acquisition (DDA) mode, where typically 10–20 most abundant ions found in MS are subsequently selected for fragmentation in MS/MS to enable peptide identification (18). Although this discovery-mode (or shotgun) proteomic approach provides the potential to uncover novel protein targets, sample complexity, together with inherent variation in automated peak selection, results in compromised sensitivity and reproducibility for protein quantification. As a result, only partially overlapping sets of proteins can be identified even from substantially similar samples (11). The inadequate sensitivity and reproducibility of these kinome detection strategies hamper their utility in biomarker discovery and clinical studies.Targeted proteomics technique, which relies on multiple-reaction monitoring (MRM) on triple quadrupole mass spectrometers, has become increasingly used in quantitative proteomics studies (19). In the MRM mode, mass filtering of both the precursor and product ions is employed to provide high specificity for the quantification of target proteins. Additionally, this MRM-based targeted MS analysis permits rapid and continuous monitoring of specific ions of interest, which enhances the sensitivity for peptide detection by up to 100-fold relative to MS analysis in DDA-based discovery mode (20). Therefore, the MRM-based targeted proteomic approach may enable global kinome profiling with high specificity, sensitivity, throughput, and reproducibility.Here, we developed the first MRM-based platform to support the multiplexed, reproducible, and sensitive quantification of ∼300 protein kinases in the human kinome. Aside from conventional MRM-based assay design, we selectively label and enrich kinases from complex human proteome prior to MRM analysis with the use of desthiobiotin-based isotope-coded ATP-affinity probe (ICAP) (21) to attain high specificity and sensitivity. We demonstrated that this MRM-based kinome detection strategy coupled with ICAP reagent is applicable for clinical samples that are not amenable to metabolic labeling. Additionally, this MRM-based kinome assay is easily transferable between instruments and laboratories, rendering it a facile and universal strategy for global kinome detection.     

Tissue Profiling of the Mammalian Central Nervous System Using Human Antibody-based Proteomics

A need exists for mapping the protein profiles in the human brain both during normal and disease conditions. Here we studied 800 antibodies generated toward human proteins as part of a Human Protein Atlas program and investigated their suitability for detailed analysis of various levels of a rat brain using immuno-based methods. In this way, the parallel, rather limited analysis of the human brain, restricted to four brain areas (cerebellum, cerebral cortex, hippocampus, and lateral subventricular zone), could be extended in the rat model to 25 selected areas of the brain. Approximately 100 antibodies (12%) revealed a distinct staining pattern and passed validation of specificity using Western blot analysis. These antibodies were applied to coronal sections of the rat brain at 0.7-mm intervals covering the entire brain. We have now produced detailed protein distribution profiles for these antibodies and acquired over 640 images that form the basis of a publicly available portal of an antibody-based Rodent Brain Protein Atlas database (www.proteinatlas.org/rodentbrain). Because of the systematic selection of target genes, the majority of antibodies included in this database are generated against proteins that have not been studied in the brain before. Furthermore optimized tissue processing and colchicine treatment allow a high quality, more extended annotation and detailed analysis of subcellular distributions and protein dynamics.The brain is the most complex organ in the mammalian body. It processes sensory information from our external environment; produces behavior, emotions, and memories; and regulates the internal body homeostasis. To fulfill these diverse functions the brain harbors a myriad of neuronal networks processing information and connecting input and output systems. Because of the highly specialized functions, each neuron population is neurochemically specified expressing the necessary sets of proteins. Consequently a large number of genes are expressed in the mammalian brain. Based on microarray and in situ hybridization studies it is estimated that ∼55–80% of all mouse genes are expressed in the brain (1, 2) (gene expression during developmental stages and pathological conditions not included). Interestingly 70% of these genes are expressed in different cell populations each covering less than 20% of the brain, indicating the complexity of the brain and the specialization of individual populations of neurons (1).The success of humans as a species relies on our mental abilities, a result of brain development during evolution. The human brain is distinguished from other mammalian brains by its size; especially the neocortex involved in higher cognitive functions is greatly enlarged in humans. Despite this difference, the human brain has many similarities to brains of other mammalian species, and to some extent mammalian brains have a well preserved basic architecture (basic uniformity) (for reviews, see Refs. 3 and 4). Therefore, most human brain nuclei and connections have orthologs in other mammalian species ranging from great apes to rodents.Genetic variation underpins interspecies variation in gene expression and assembly of proteins. The human and rat genomes encode similar numbers of genes of which the majority have persisted throughout evolution without deletion or duplication (5). It is evident that small changes in protein structure and altered expression levels of proteins influence brain development and form the basis of interspecies differences. However, most human genes have orthologs in rodents, and for most cell types in the brain their neurochemical specification has been preserved throughout evolution. Because of genomic homology and similarity in basic layout of the mammalian brain as well as the preservation of neurochemical specification of subsets of neurons throughout evolution, animal models have shown their value in medical neurosciences (6).Advances in science are largely dependent on the processing of available information and the generation of new concepts and are driven by innovation and availability of new technologies. Recently mRNA-based techniques have emerged as an effective tool for genome wide analysis of expression levels in entire organs or disease-affected tissue. Results obtained from these studies are a source for identification of novel key molecules and have a predictive value to estimate changes in protein synthesis. There are several ongoing initiatives focusing on the expression profiles of the mammalian brain. The Allen Brain Atlas has produced detailed in situ hybridization profiles for over 20,000 genes in the mouse brain (1). The Gene Expression Nervous System Atlas (GENSAT) project uses enhanced green fluorescent protein reporter genes incorporated into bacterial artificial chromosome transgenic mice to visualize the expression profiles of the most important genes (7). This strategy can result in the identification of expressing cell types as the detailed morphology of enhanced green fluorescent protein-expressing cells is apparent. The Brain Maps project has a large collection of mammalian and non-mammalian brain maps using “classical” histochemical techniques but also includes a few protein distribution profiles visualized using immunohistochemistry (8).We previously described the possibilities of using antibodies raised against human proteins on rodent brain tissue (9). Here we show the first efforts to produce detailed proteome wide large scale tissue profiling maps of a mammalian brain using an antibody-based proteomics approach. In addition to the available, mentioned information on mRNA levels (Allen Brain Atlas), gene expression profiles (Gene Expression Nervous System Atlas), and detailed neuroanatomy (Brain Maps), antibody-based proteomics provide new information on cellular and subcellular distribution of gene products. This information will increase general knowledge and understanding of the organization and functioning of the brain. The study is based on antibodies generated as part of the Human Protein Atlas program aimed at exploring the protein expression patterns in normal and cancer tissues using tissue microarray-based immunohistochemistry and fluorescence-based confocal microscopy (10).The Human Proteome Resource center aims to produce monospecific antibodies against every human gene. So far, the distribution profiles of 3,000 proteins in 48 human tissues, including four brain areas (cerebellum, cerebral cortex, the hippocampal formation, and lateral subventricular zone), and 20 cancers are available (Human Protein Atlas). The antibodies generated within the framework of this program are based on antigens selected as unique regions for each individual protein, called protein epitope signature tags (PrESTs)¹ (11, 12). Over 5,000 antibodies have been generated and validated using Western blot analysis and protein arrays (13). The smaller size of the rat brain allows analysis of many brain areas and exposure of the antibodies to a very wide variety of proteins. Furthermore tissue can be processed under perfect conditions optimizing tissue antigenicity with flawless tissue morphology.Here we describe the initial large scale mapping of 89 protein distribution profiles in 25 selected rat brain areas. By exposing systematically sampled rat brain tissue to our collection of monospecific antibodies a more detailed protein atlas of the mammalian brain was produced, expanding the four brain areas available in the human protein atlas to 25 brain areas (Fig. 1) involved in higher cognitive functions, sensation, emotion, maintenance of internal homeostasis, sleep, and motor and sexual behaviors. A database portal has been created to show selected images from the various regions of the brain.Open in a separate windowFig. 1.Schematic overview of the 25 selected brain areas. Included are telencephalon (medial septum, lateral septum, horizontal/vertical diagonal band, prefrontal/cingulate/somatosensory/piriform/entorhinal cortex, ventral pallidum, stria terminalis, globus pallidus, caudate putamen, amygdala (basolateral, central, and medial), hippocampus, and dentate gyrus); diencephalon (preoptic area (A), supraoptic nucleus (A), suprachiasmatic nucleus (A), paraventricular nucleus (A and B), arcuate nucleus (B), median eminence (B), and thalamus); mesencephalon (substantia nigra, ventral tegmental area, and raphe nucleus (dorsal and median)); pons (locus caeruleus (C)); and cerebellum.